fix: configure setuptools package discovery for src layout

[fmueller]

Motivation

• Ensure build tools can discover and install the package from the repository's src layout by configuring setuptools package discovery and including package data in the distribution.

Description

• Add a [tool.setuptools] section to pyproject.toml with package-dir = { "" = "src" }, include-package-data = true, and a packages.find config with where = ["src"] so setuptools can find packages under src.

Testing

• Ran uv run ruff check (passed), uv run pytest (160 tests passed), and uv run mypy which failed due to missing torch because uv sync --locked --all-extras --dev could not download mpmath (network/tunnel error) preventing installation of the extra required for type-checking.

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Codex Task